Details aside, I think you should just choose one system and stick with it, and make any necessary changes from scratch.
It sounds to me as though you've set your heart on using D20, so I'll go ahead and add my two bits since thats the only system I've any real familiarity with anyway.
The major problem with using D20 for a superhero game, that I can see, is that in D20 everything is dynamic -- there are no static abilities. The closest is feats, but you can choose one or more new feats with each level gain.
So you'd probably have to use a new set of abilities called something like "Powers." Because I'm bored I even came up with an example Power to illustrate. I should hope the source would be obvious.
Hulking BeastDescription: When angry, the character transforms into a hulking creature with immense strength, and flies into a rage.
When overcome by anger, the character grows one Size larger (i.e. from Medium to Large). Instead of the standard size modifier to STR, the character's old STR is exactly doubled. The character also flies into a rage, incurring all the standard benefits and penalties of the Barbarian special ability Rage.
Uses per Day: 1 per level
Duration: Maximum 10 minutes per level, or until ended by player.
Ok, I'm not much of an Incredible Hulk fan, nor do I have access to my D&D books right now, so this is not going to be perfect, but after all its just an example.